Contacts of the strand formed by residues 152 - 159 (chain E) in PDB entry 5MGS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E PHE* 3.9 24.5 - + + -
109E SER 4.1 3.6 - - - -
145E ILE* 3.9 40.8 - - + -
150E ILE* 3.8 25.6 - - + -
151E LEU* 1.3 75.7 - - - +
153E TRP* 1.3 64.6 + - - +
154E ILE* 3.9 2.1 - - - +
191E SER* 3.1 4.3 - - - -
192E ILE* 2.9 37.0 + - + +
207E ARG* 3.2 35.4 - - + +
208E TRP* 3.8 6.3 - - - -
209E ILE* 3.5 36.6 - - + -
91H LEU* 4.0 18.2 - - + -
92H LEU* 4.9 0.7 - - + -
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Residues in contact with TRP 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ASN 3.0 21.6 + - - -
115E TRP* 3.3 32.0 - + + +
118E SER* 3.3 24.7 - - - +
129E LEU* 4.2 2.6 - - + +
152E PHE* 1.3 74.6 - - - +
154E ILE* 1.3 61.5 + - - +
189E CYS* 3.2 35.7 - - + -
190E ILE 3.4 20.4 - - - -
191E SER 4.2 0.2 - - - -
200E GLU* 3.7 18.6 - - + -
201E TYR 3.4 22.7 - - - -
202E CYS* 3.7 8.1 - - - -
204E THR* 3.3 19.3 - - - -
206E ILE* 3.4 22.0 - - + +
207E ARG 2.8 22.1 + - - -
208E TRP* 3.6 10.3 - - + +
209E ILE* 3.2 25.6 + - - +
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Residues in contact with ILE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 2.9 18.9 + - - -
129E LEU* 4.1 5.4 - - - -
130E LEU* 3.6 36.3 - - + +
132E ILE* 3.8 21.1 - - + -
152E PHE 3.9 8.5 - - - +
153E TRP* 1.3 78.3 - - - +
155E GLY* 1.3 59.4 + - - +
156E LEU* 2.9 14.7 + - + +
167E TRP* 4.0 17.9 - - + -
178E LEU* 4.8 4.0 - - + -
190E ILE* 3.1 45.0 + - + +
192E ILE* 3.9 21.8 - - + -
209E ILE* 4.9 1.3 - - + -
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Residues in contact with GLY 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 4.4 0.2 - - - -
129E LEU* 3.5 24.6 - - - +
130E LEU 2.9 18.5 + - - -
154E ILE* 1.3 67.5 - - - +
156E LEU* 1.3 57.3 + - - -
167E TRP* 3.2 12.6 - - - -
168E ILE* 2.9 46.0 + - - +
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Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 3.8 6.7 + - - +
154E ILE* 2.9 8.2 + - + +
155E GLY* 1.3 74.6 - - - -
157E ASN* 1.3 63.4 + - - +
165E TRP* 3.8 10.8 - - + -
166E LYS 3.4 35.4 - - - +
167E TRP* 3.6 35.4 - - + +
173E LEU* 4.3 12.6 - - + -
178E LEU* 3.7 29.2 - - + -
180E ILE* 4.7 1.1 - - + -
189E CYS* 3.8 0.5 - - - -
190E ILE* 3.0 55.9 + - + +
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Residues in contact with ASN 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E TRP* 3.5 11.5 - - + -
156E LEU* 1.3 77.0 - - - +
158E PHE* 1.3 65.9 + - - +
159E SER* 3.6 1.0 + - - -
165E TRP* 3.3 9.6 - - - -
166E LYS* 2.8 46.6 + - - +
168E ILE* 5.9 0.6 - - - +
188E SER 3.6 4.7 - - - +
189E CYS* 3.5 21.5 - - - -
202E CYS* 4.8 0.2 - - - -
502E NAG 1.5 68.4 + - - +
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Residues in contact with PHE 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ASN* 1.3 79.1 - - - +
159E SER* 1.3 66.6 - - - +
160E LEU* 3.7 24.8 + - + +
163E LYS* 3.5 26.0 - - + -
164E ASN* 3.4 28.3 - - - -
165E TRP* 3.5 15.2 - + + -
184E ALA* 3.3 42.4 - - + -
185E LYS* 3.2 31.9 - - - +
186E GLU* 4.0 4.9 - - - -
187E ASN 5.2 4.5 + - - -
188E SER 3.0 17.4 + - - +
502E NAG 5.0 8.0 + - - +
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Residues in contact with SER 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ASN* 3.6 1.9 + - - -
158E PHE* 1.3 70.9 - - - +
160E LEU* 1.3 61.3 + - - +
161E SER* 3.4 4.5 - - - -
162E GLU* 2.8 24.1 + - - -
163E LYS* 2.9 24.8 + - - -
164E ASN 2.9 22.0 + - - -
166E LYS* 3.7 33.8 - - - -
172E PHE* 4.4 4.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il